Merge pull request #295 from DeepSenseCA/rel_1.1.0

REL: Release version 1.1.0

.coveragerc

@@ -0,0 +1,23 @@
+[run]
+branch = True
+omit = */tests/*
+
+[report]
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    if self\.debug:
+    if debug:
+    if DEBUG:
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if False:
+    if __name__ == .__main__.:

.flake8

@@ -1,5 +1,12 @@
 [flake8]
 max-line-length = 120
-# C408 ignored because we like the dict keyword argument syntax
-ignore = E203,E305,E402,E721,E741,F401,F403,F405,F821,F841,F999,W503,W504,C408
-exclude = docs/src,venv,third_party,caffe2,scripts,docs/caffe2,tools/amd_build/pyHIPIFY,torch/lib/include,torch/lib/tmp_install,build,torch/include
+# C408 ignored because pytorch likes the dict keyword argument syntax
+# E203: whitespace before ":". Sometimes violated by black.
+# E402: Module level import not at top of file. Violated by lazy imports.
+# F401: Module imported but unused.
+# D100-D107: Missing docstrings
+# D200: One-line docstring should fit on one line with quotes.
+extend-ignore = C408,E203,E402,F401,D100,D101,D102,D103,D104,D105,D106,D107,D200
+docstring-convention = numpy
+# Ignore missing docstrings within unit testing functions.
+per-file-ignores = **/tests/:D100,D101,D102,D103,D104,D105,D106,D107

.gitattributes

@@ -1,57 +1,86 @@
 ##---------------------------------------------------
 # Common .gitattributes
 ##---------------------------------------------------
+# Common settings that generally should always be used with your language specific settings
 
 # Auto detect text files and perform LF normalization
-* text=auto
+# https://www.davidlaing.com/2012/09/19/customise-your-gitattributes-to-become-a-git-ninja/
+*           text=auto
 
 #
 # The above will handle all files NOT found below
 #
 
 # Documents
-# ============
-*.doc	    diff=astextplain
-*.DOC	    diff=astextplain
+*.bibtex    text diff=bibtex
+*.doc       diff=astextplain
+*.DOC       diff=astextplain
 *.docx      diff=astextplain
 *.DOCX      diff=astextplain
 *.dot       diff=astextplain
 *.DOT       diff=astextplain
 *.pdf       diff=astextplain
-*.PDF	    diff=astextplain
-*.rtf	    diff=astextplain
-*.RTF	    diff=astextplain
-*.md        text
-*.tex       text
+*.PDF       diff=astextplain
+*.rtf       diff=astextplain
+*.RTF       diff=astextplain
+*.md        text diff=markdown
+*.tex       text diff=tex
 *.adoc      text
 *.textile   text
 *.mustache  text
 *.csv       text
 *.tab       text
 *.tsv       text
+*.txt       text
 *.sql       text
+*.ps1       text eol=crlf
 
 # Graphics
-# ============
 *.png       binary
 *.jpg       binary
 *.jpeg      binary
 *.gif       binary
 *.tif       binary
 *.tiff      binary
 *.ico       binary
-# SVG treated as an asset (binary) by default. If you want to treat it as text,
-# comment-out the following line and uncomment the line after.
-*.svg       binary
-#*.svg      text
+# SVG treated as an asset (text) by default.
+*.svg       text
+# If you want to treat it as binary, use the following line instead.
+# *.svg     binary
 *.eps       binary
 
+# Scripts
+*.bash      text eol=lf
+*.fish      text eol=lf
+*.sh        text eol=lf
+# These are explicitly windows files and should use crlf
+*.bat       text eol=crlf
+*.cmd       text eol=crlf
+
+# Serialisation
+*.json      text
+*.toml      text
+*.xml       text
+*.yaml      text
+*.yml       text
+
+# Archives
+*.7z        binary
+*.gz        binary
+*.tar       binary
+*.tgz       binary
+*.zip       binary
+
+# Text files where line endings should be preserved
+*.patch     -text
+
 #
 # Exclude files from exporting
 #
 
 .gitattributes export-ignore
-.gitignore export-ignore
+.gitignore     export-ignore
+.gitkeep       export-ignore
 
 
 ##---------------------------------------------------
@@ -73,9 +102,9 @@
 *.db        binary
 *.p         binary
 *.pkl       binary
-*.pyc       binary
+*.pyc       binary export-ignore
+*.pyo       binary export-ignore
 *.pyd       binary
-*.pyo       binary
 
 # Note: .db, .p, and .pkl files are associated
 # with the python modules ``pickle``, ``dbm.*``,
@@ -84,5 +113,12 @@
 
 # Jupyter Notebooks
 # =================
-*.ipynb filter=nbstripout
-*.ipynb diff=ipynb
+*.ipynb     text
+
+
+##---------------------------------------------------
+# Project specific
+##---------------------------------------------------
+
+# Don't manipulate test resources
+test-resources/*  binary

.github/workflows/docs.yaml

@@ -0,0 +1,40 @@
+# Docs workflow
+#
+# Ensures that the docs can be built with sphinx.
+# - On every push and PR, checks the HTML documentation builds on linux.
+# - On every PR and tag, checks the documentation builds as a PDF on linux.
+# - If your repository is public, on pushes to the default branch (i.e. either
+#   master or main), the HTML documentation is pushed to the gh-pages branch,
+#   which is automatically rendered at the publicly accessible url
+#   https://USER.github.io/PACKAGE/
+
+name: docs
+
+on: [push, pull_request]
+
+jobs:
+  docs-html:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Check if README.md needs to be converted
+      id: check_readme
+      run: |
+        if [ ! -f "README.rst" ] && [ -f "README.md" ]; then
+            echo '::set-output name=convert::true';
+        fi
+
+    - name: Convert README.md to README.rst
+      if: steps.check_readme.outputs.convert == 'true'
+      uses: docker://pandoc/core:2.9
+      with:
+        args: >-
+            README.md
+            --from=gfm
+            --output=README.rst
+
+    - name: Build HTML docs
+      uses: ammaraskar/sphinx-action@master
+      with:
+        docs-folder: "docs/"

.github/workflows/system_info.py

@@ -0,0 +1,21 @@
+"""
+Print out some handy system info.
+"""
+
+import os
+import platform
+import sys
+
+print("Build system information")
+print()
+
+print("sys.version\t\t", sys.version.split("\n"))
+print("os.name\t\t\t", os.name)
+print("sys.platform\t\t", sys.platform)
+print("platform.system()\t", platform.system())
+print("platform.machine()\t", platform.machine())
+print("platform.platform()\t", platform.platform())
+print("platform.version()\t", platform.version())
+print("platform.uname()\t", platform.uname())
+if sys.platform == "darwin":
+    print("platform.mac_ver()\t", platform.mac_ver())

.github/workflows/test.yaml

@@ -0,0 +1,106 @@
+# Regular tests
+#
+# Use this to ensure your tests are passing on every push and PR (skipped on
+# pushes which only affect documentation).
+# There is also a cron job set to run weekly on the default branch, to check
+# against dependency chain rot.
+#
+# You should make sure you run jobs on at least the *oldest* and the *newest*
+# versions of python that your codebase is intended to support.
+
+name: tests
+
+on:
+  push:
+  pull_request:
+  schedule:
+    - cron:  "0 0 * * 1"
+      branches: [ $default-branch ]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.6", "3.7"]
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python-version }}
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: System information
+      run: python .github/workflows/system_info.py
+
+    - name: Get pip cache dir
+      id: pip-cache
+      run: echo "::set-output name=dir::$(pip cache dir)"
+
+    - name: pip cache
+      uses: actions/cache@v2
+      with:
+        path: ${{ steps.pip-cache.outputs.dir }}
+        key: ${{ runner.os }}-pip-py${{ matrix.python-version }}-${{ hashFiles('**/requirements*.txt') }}
+        restore-keys: ${{ runner.os }}-pip-
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8
+        python -m pip install torch==1.4.0+cpu torchvision==0.5.0+cpu -f https://download.pytorch.org/whl/torch_stable.html
+        python -m pip install -r frozen_requirements.txt
+        python -m pip install .[test]
+
+    - name: Get appdirs cache dir
+      id: appdirs-cache
+      run: echo "::set-output name=dir::$(python -c 'from echofilter.ui.checkpoints import get_default_cache_dir as c; print(c())')"
+
+    - name: Cache checkpoints
+      uses: actions/cache@v3
+      with:
+        path: ${{ steps.appdirs-cache.outputs.dir }}
+        key: checkpoints-${{ hashFiles('**/echofilter/checkpoints.yaml') }}
+        restore-keys: checkpoints-
+
+    - name: Sanity check with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        python -m flake8 . --count --select=E9,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings
+        python -m flake8 . --count --exit-zero --statistics
+
+    - name: Debug environment
+      run: python -m pip freeze
+
+    - name: Test with pytest
+      run: |
+        python -m pytest --cov=echofilter --cov-report term --cov-report xml --cov-config .coveragerc --junitxml=testresults.xml
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1
+      with:
+        flags: unittests
+        env_vars: OS,PYTHON
+        name: Python ${{ matrix.python-version }} on ${{ runner.os }}
+
+    - name: Test show help
+      run: echofilter -h
+
+    - name: Test show version
+      run: echofilter --version
+
+    - name: Test list-checkpoints
+      run: echofilter --list-checkpoints
+
+    - name: Test list-colors
+      run: echofilter --list-colors
+
+    - name: Test dry-run
+      run: echofilter test-resources -n

.gitignore

@@ -14,13 +14,38 @@ echofilter/checkpoints
 # Auto-generated rST root file for exporting docs to PDF
 docs/index_pdf.rst
 
+# Ignore all built documentation (including Guide and PDF)
+docs/_build*
+
+# Ignore extra directories
+image_samples/
+models/
+notes/
+processed/
+results/
+test-output/
+test-resources-source/
+
+
+##---------------------------------------------------
+# Automated documentation .gitignore files
+##---------------------------------------------------
+
+# Automatically generated API documentation stubs from sphinx-apidoc
+docs/source/packages
+
+# Automatically converting README from markdown to rST
+docs/bin
+docs/source/readme.rst
+
 
 ##---------------------------------------------------
 # Continuous Integration .gitignore files
 ##---------------------------------------------------
 
 # Ignore test result XML files
 testresults.xml
+coverage.xml
 
 
 ##---------------------------------------------------
@@ -97,9 +122,6 @@ instance/
 
 # Sphinx documentation
 docs/_build/
-docs/_build*
-# sphinx-apidoc automatically generated documentation
-docs/source/packages
 
 # PyBuilder
 target/
@@ -154,6 +176,9 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
+# pytype static type analyzer
+.pytype/
+
 
 ##---------------------------------------------------
 # Windows default .gitignore